[lammps] branch master updated (eb0d0ab -> 32b9d4b)
Anton Gladky
gladk at moszumanska.debian.org
Sat May 24 19:14:18 UTC 2014
This is an automated email from the git hooks/post-receive script.
gladk pushed a change to branch master
in repository lammps.
from eb0d0ab Update changelog.
new 4c132dc Grab source from GitHub page.
new 7811c49 Move mpi-default-bin to Depends.
adds 4bd2ecb Imported Upstream version 0~20140523.gite5e877d
new 7653943 Merge tag 'upstream/0_20140523.gite5e877d'
new 7f4e9a8 Remove colloid autopkgtest.
new 32b9d4b Update changelog.
The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
debian/changelog | 9 +
debian/control | 6 +-
debian/scripts/get_orig_src.sh | 2 +-
debian/tests/colloid | 71 -
debian/tests/control | 2 +-
doc/Eqs/compute_fep_bar.jpg | Bin 0 -> 18106 bytes
doc/Eqs/compute_fep_bar.tex | 7 +
doc/Eqs/compute_fep_fdti.jpg | Bin 0 -> 15544 bytes
doc/Eqs/compute_fep_fdti.tex | 10 +
doc/Eqs/compute_fep_fep.jpg | Bin 0 -> 18055 bytes
doc/Eqs/compute_fep_fep.tex | 9 +
doc/Eqs/compute_fep_lambda.jpg | Bin 0 -> 10511 bytes
doc/Eqs/compute_fep_lambda.tex | 10 +
doc/Eqs/compute_fep_ti.jpg | Bin 0 -> 18149 bytes
doc/Eqs/compute_fep_ti.tex | 10 +
doc/Eqs/compute_fep_u.jpg | Bin 0 -> 9337 bytes
doc/Eqs/compute_fep_u.tex | 7 +
doc/Eqs/compute_fep_vol.jpg | Bin 0 -> 15209 bytes
doc/Eqs/compute_fep_vol.tex | 9 +
doc/Eqs/pair_coul_soft.jpg | Bin 0 -> 11309 bytes
doc/Eqs/pair_coul_soft.tex | 10 +
doc/Eqs/pair_lj_soft.jpg | Bin 0 -> 17984 bytes
doc/Eqs/pair_lj_soft.tex | 15 +
doc/JPG/coul_soft.jpg | Bin 0 -> 12676 bytes
doc/JPG/lj_soft.jpg | Bin 0 -> 12313 bytes
doc/Manual.html | 4 +-
doc/Manual.txt | 4 +-
doc/PDF/colvars-refman-lammps.pdf | Bin 592707 -> 601866 bytes
doc/Section_commands.html | 131 +-
doc/Section_commands.txt | 30 +-
doc/Section_errors.html | 26 +-
doc/Section_errors.txt | 26 +-
doc/Section_howto.html | 5 +
doc/Section_howto.txt | 5 +
doc/Section_modify.html | 177 +-
doc/Section_modify.txt | 179 +-
doc/Section_packages.html | 26 +-
doc/Section_packages.txt | 26 +-
doc/Section_python.html | 10 +-
doc/Section_python.txt | 10 +-
doc/Section_start.html | 33 +-
doc/Section_start.txt | 33 +-
doc/Section_tools.html | 14 +
doc/Section_tools.txt | 14 +
doc/balance.html | 284 +-
doc/balance.txt | 285 +-
doc/{communicate.html => comm_modify.html} | 57 +-
doc/{communicate.txt => comm_modify.txt} | 54 +-
doc/comm_style.html | 70 +
doc/comm_style.txt | 65 +
doc/compute_fep.html | 274 +
doc/compute_fep.txt | 258 +
doc/compute_gyration.html | 3 +-
doc/compute_gyration.txt | 3 +-
doc/compute_gyration_molecule.html | 3 +-
doc/compute_gyration_molecule.txt | 3 +-
doc/compute_modify.html | 4 +-
doc/compute_modify.txt | 4 +-
doc/compute_property_atom.html | 7 +-
doc/compute_property_atom.txt | 7 +-
doc/compute_vacf.html | 2 +-
doc/compute_vacf.txt | 2 +-
doc/compute_voronoi_atom.html | 45 +-
doc/compute_voronoi_atom.txt | 44 +-
doc/create_atoms.html | 2 +
doc/create_atoms.txt | 2 +
doc/create_box.html | 22 +-
doc/create_box.txt | 22 +-
doc/delete_atoms.html | 19 +-
doc/delete_atoms.txt | 19 +-
doc/dump.html | 19 +-
doc/dump.txt | 19 +-
doc/dump_image.html | 66 +-
doc/dump_image.txt | 67 +-
doc/dump_modify.html | 10 +-
doc/dump_modify.txt | 10 +-
doc/fix_adapt.html | 10 +-
doc/fix_adapt.txt | 10 +-
doc/{fix_adapt.html => fix_adapt_fep.html} | 63 +-
doc/{fix_adapt.txt => fix_adapt_fep.txt} | 63 +-
doc/fix_balance.html | 249 +-
doc/fix_balance.txt | 247 +-
doc/fix_bond_break.html | 11 +-
doc/fix_bond_break.txt | 11 +-
doc/fix_bond_create.html | 112 +-
doc/fix_bond_create.txt | 112 +-
doc/fix_bond_swap.html | 10 +-
doc/fix_bond_swap.txt | 10 +-
doc/fix_deposit.html | 42 +-
doc/fix_deposit.txt | 42 +-
doc/fix_evaporate.html | 5 +
doc/fix_evaporate.txt | 5 +
doc/fix_gcmc.html | 25 +-
doc/fix_gcmc.txt | 25 +-
doc/fix_pour.html | 28 +-
doc/fix_pour.txt | 28 +-
doc/fix_reaxc_species.html | 128 +-
doc/fix_reaxc_species.txt | 129 +-
doc/fix_restrain.html | 2 +-
doc/fix_restrain.txt | 2 +-
doc/fix_rigid.html | 49 +-
doc/fix_rigid.txt | 45 +-
doc/fix_thermal_conductivity.html | 2 +-
doc/fix_thermal_conductivity.txt | 2 +-
doc/fix_vector.html | 2 +-
doc/fix_vector.txt | 2 +-
doc/group.html | 6 +
doc/group.txt | 6 +
doc/pair_coul_diel.html | 2 +
doc/pair_coul_diel.txt | 1 +
doc/pair_lj_long.html | 4 +-
doc/pair_lj_long.txt | 4 +-
doc/pair_lj_soft.html | 280 +
doc/pair_lj_soft.txt | 258 +
doc/pair_reax_c.html | 4 -
doc/pair_reax_c.txt | 4 -
doc/processors.html | 51 +-
doc/processors.txt | 51 +-
doc/read_data.html | 7 +-
doc/read_data.txt | 7 +-
doc/read_dump.html | 2 +-
doc/read_dump.txt | 2 +-
doc/read_restart.html | 10 +-
doc/read_restart.txt | 10 +-
doc/replicate.html | 7 +-
doc/replicate.txt | 7 +-
doc/rerun.html | 24 +-
doc/rerun.txt | 22 +-
doc/restart.html | 11 +
doc/restart.txt | 11 +
doc/run.html | 8 +-
doc/run.txt | 8 +-
doc/special_bonds.html | 11 +-
doc/special_bonds.txt | 11 +-
doc/thermo_style.html | 30 +-
doc/thermo_style.txt | 30 +-
doc/variable.html | 66 +-
doc/variable.txt | 66 +-
examples/README | 1 +
examples/USER/awpmd/H/in.h_atom | 2 +-
examples/USER/awpmd/H/in.h_molecule | 2 +-
examples/USER/cg-cmm/sds-monolayer/in.sds-hybrid | 2 +-
examples/USER/fep/CC-CO/README | 87 +
examples/USER/fep/CC-CO/bar01/bar01.lmp | 5003 +++++++++++
examples/USER/fep/CC-CO/bar01/in.bar01.lmp | 120 +
examples/USER/fep/CC-CO/bar01/log.lammps | 6857 +++++++++++++++
examples/USER/fep/CC-CO/bar10/bar10.lmp | 5003 +++++++++++
examples/USER/fep/CC-CO/bar10/in.bar10.lmp | 120 +
examples/USER/fep/CC-CO/bar10/log.lammps | 6857 +++++++++++++++
examples/USER/fep/CC-CO/fdti01/fdti01.lmp | 22 +
examples/USER/fep/CC-CO/fdti01/in.fdti01.lmp | 142 +
examples/USER/fep/CC-CO/fdti01/log.lammps | 6321 ++++++++++++++
examples/USER/fep/CC-CO/fdti10/fdti10.lmp | 22 +
examples/USER/fep/CC-CO/fdti10/in.fdti10.lmp | 142 +
examples/USER/fep/CC-CO/fdti10/log.lammps | 6321 ++++++++++++++
examples/USER/fep/CC-CO/fep01/data.0.lmp | 2275 +++++
examples/USER/fep/CC-CO/fep01/fep01.lmp | 22 +
examples/USER/fep/CC-CO/fep01/in.fep01 | 143 +
examples/USER/fep/CC-CO/fep01/in.fep01.lmp | 142 +
examples/USER/fep/CC-CO/fep01/log.lammps | 6321 ++++++++++++++
examples/USER/fep/CC-CO/fep01/log.reference | 285 +
examples/USER/fep/CC-CO/fep01/log.reference-omp | 287 +
examples/USER/fep/CC-CO/fep10/fep10.lmp | 22 +
examples/USER/fep/CC-CO/fep10/in.fep10.lmp | 142 +
examples/USER/fep/CC-CO/fep10/log.lammps | 6321 ++++++++++++++
examples/USER/fep/CC-CO/mols/CC-CO.ff | 49 +
examples/USER/fep/CC-CO/mols/CC-CO.zmat | 14 +
examples/USER/fep/CC-CO/mols/CO-CC.zmat | 14 +
examples/USER/fep/CC-CO/mols/README | 15 +
examples/USER/fep/CC-CO/mols/data.0.lmp | 2275 +++++
examples/USER/fep/CC-CO/mols/data.1.lmp | 2275 +++++
examples/USER/fep/CC-CO/mols/spce.ff | 14 +
examples/USER/fep/CC-CO/mols/spce.zmat | 7 +
examples/USER/fep/CH4-CF4/README | 57 +
examples/USER/fep/CH4-CF4/bar01/bar01.lmp | 5003 +++++++++++
examples/USER/fep/CH4-CF4/bar01/in.bar01.lmp | 89 +
examples/USER/fep/CH4-CF4/bar01/log.lammps | 6514 ++++++++++++++
examples/USER/fep/CH4-CF4/bar10/bar10.lmp | 5003 +++++++++++
examples/USER/fep/CH4-CF4/bar10/in.bar10.lmp | 89 +
examples/USER/fep/CH4-CF4/bar10/log.lammps | 6514 ++++++++++++++
examples/USER/fep/CH4-CF4/mols/CF4-CH4.zmat | 16 +
examples/USER/fep/CH4-CF4/mols/CH4-CF4.ff | 28 +
examples/USER/fep/CH4-CF4/mols/CH4-CF4.zmat | 16 +
examples/USER/fep/CH4-CF4/mols/data.0.lmp | 2249 +++++
examples/USER/fep/CH4-CF4/mols/data.1.lmp | 2249 +++++
examples/USER/fep/CH4-CF4/mols/spce.ff | 14 +
examples/USER/fep/CH4-CF4/mols/spce.zmat | 7 +
examples/USER/fep/CH4hyd/README | 59 +
examples/USER/fep/CH4hyd/fdti01/fdti01.lmp | 22 +
examples/USER/fep/CH4hyd/fdti01/in.fdti01.lmp | 80 +
examples/USER/fep/CH4hyd/fdti01/log.lammps | 5156 +++++++++++
examples/USER/fep/CH4hyd/fdti10/fdti10.lmp | 22 +
examples/USER/fep/CH4hyd/fdti10/in.fdti10.lmp | 80 +
examples/USER/fep/CH4hyd/fdti10/log.lammps | 5156 +++++++++++
examples/USER/fep/CH4hyd/fep01/fep01.lmp | 22 +
examples/USER/fep/CH4hyd/fep01/in.fep01.lmp | 80 +
examples/USER/fep/CH4hyd/fep01/log.lammps | 5156 +++++++++++
examples/USER/fep/CH4hyd/fep10/fep10.lmp | 22 +
examples/USER/fep/CH4hyd/fep10/in.fep10.lmp | 80 +
examples/USER/fep/CH4hyd/fep10/log.lammps | 5156 +++++++++++
examples/USER/fep/CH4hyd/mols/data.lmp | 2215 +++++
examples/USER/fep/CH4hyd/mols/methane.zmat | 9 +
examples/USER/fep/CH4hyd/mols/oplsaa.ff | 85 +
examples/USER/fep/CH4hyd/mols/tip4pew.ff | 14 +
examples/USER/fep/CH4hyd/mols/tip4pew.zmat | 7 +
examples/USER/fep/README | 11 +
examples/USER/phonon/1-1D-mono/in.Ana | 2 +-
examples/USER/phonon/2-1D-diatomic/in.Ana | 2 +-
examples/VISCOSITY/in.gk.2d | 19 +-
examples/colloid/in.colloid | 2 +-
examples/comb/in.comb3 | 2 +-
examples/comb/log.comb3.1Feb14.linux.1 | 48 +-
examples/comb/log.comb3.1Feb14.linux.4 | 54 +-
examples/nb3b/MOH.nb3b.harmonic | 20 +
examples/nb3b/data.nb3b | 1991 +++++
examples/nb3b/in.nb3b | 49 +
examples/nb3b/log.nb3b.1Feb14.linux.1 | 144 +
examples/nb3b/log.nb3b.1Feb14.linux.4 | 144 +
examples/pour/in.pour | 2 +-
examples/pour/in.pour.2d | 2 +-
examples/pour/in.pour.2d.molecule | 2 +-
examples/srd/in.srd.mixture | 2 +-
examples/srd/in.srd.pure | 2 +-
examples/voronoi/in.voronoi | 71 +-
lib/colvars/colvar.cpp | 7 +-
lib/colvars/colvaratoms.cpp | 6 +-
lib/colvars/colvaratoms.h | 4 +-
lib/colvars/colvarbias.cpp | 4 +-
lib/colvars/colvarbias_meta.cpp | 8 +-
lib/colvars/colvarcomp.cpp | 8 +-
lib/colvars/colvargrid.h | 10 +-
lib/colvars/colvarmodule.cpp | 35 +
lib/colvars/colvarmodule.h | 36 +-
lib/colvars/colvarparse.cpp | 2 +-
lib/gpu/lal_sw.cpp | 8 +-
lib/gpu/lal_sw.cu | 79 +-
src/ASPHERE/compute_temp_asphere.cpp | 11 +-
src/ASPHERE/compute_temp_asphere.h | 2 +-
src/ASPHERE/pair_tri_lj.cpp | 4 +-
src/CLASS2/dihedral_class2.cpp | 4 +-
src/COLLOID/fix_wall_colloid.cpp | 4 +-
src/COLLOID/pair_yukawa_colloid.cpp | 6 +-
src/DIPOLE/atom_vec_dipole.cpp | 6 +-
src/DIPOLE/pair_lj_long_dipole_long.cpp | 3 +-
src/FLD/pair_brownian.cpp | 4 +-
src/FLD/pair_brownian_poly.cpp | 2 -
src/FLD/pair_lubricate.cpp | 13 +-
src/FLD/pair_lubricate_poly.cpp | 12 +-
src/GPU/pair_born_coul_long_gpu.cpp | 3 +-
src/GPU/pair_buck_coul_long_gpu.cpp | 3 +-
src/GPU/pair_coul_long_gpu.cpp | 2 +-
src/GPU/pair_dpd_tstat_gpu.cpp | 2 +-
src/GPU/pair_eam_gpu.cpp | 9 +-
src/GPU/pair_lj_sdk_coul_long_gpu.cpp | 3 +-
src/GPU/pppm_gpu.cpp | 2 +-
src/GRANULAR/fix_pour.cpp | 176 +-
src/GRANULAR/fix_pour.h | 6 +-
src/GRANULAR/pair_gran_hooke.cpp | 4 +-
src/GRANULAR/pair_gran_hooke_history.cpp | 5 +-
src/KSPACE/{commgrid.cpp => gridcomm.cpp} | 25 +-
src/KSPACE/{commgrid.h => gridcomm.h} | 12 +-
src/KSPACE/msm.cpp | 33 +-
src/KSPACE/msm.h | 8 +-
src/KSPACE/msm_cg.cpp | 3 +-
src/KSPACE/pair_lj_cut_coul_long.cpp | 1 +
src/KSPACE/pair_lj_cut_coul_msm.cpp | 1 +
src/KSPACE/pair_lj_cut_tip4p_long.cpp | 8 +-
src/KSPACE/pair_lj_long_coul_long.cpp | 5 -
src/KSPACE/pair_lj_long_tip4p_long.cpp | 59 +-
src/KSPACE/pppm.cpp | 14 +-
src/KSPACE/pppm.h | 4 +-
src/KSPACE/pppm_cg.cpp | 2 +-
src/KSPACE/pppm_disp.cpp | 56 +-
src/KSPACE/pppm_disp.h | 8 +-
src/KSPACE/pppm_disp_tip4p.cpp | 3 +-
src/KSPACE/pppm_stagger.cpp | 2 +-
src/KSPACE/remap.cpp | 13 +-
src/MAKE/Makefile.bgq | 55 +
src/MAKE/Makefile.bgq.details | 104 +
src/MAKE/Makefile.ubuntu | 112 +
src/MAKE/Makefile.ubuntu_simple | 111 +
src/MANYBODY/pair_airebo.cpp | 2 -
src/MANYBODY/pair_comb.cpp | 15 +-
src/MANYBODY/pair_comb3.cpp | 356 +-
src/MANYBODY/pair_lcbop.cpp | 10 +-
src/MC/fix_bond_break.cpp | 190 +-
src/MC/fix_bond_break.h | 5 +-
src/MC/fix_bond_create.cpp | 937 +-
src/MC/fix_bond_create.h | 34 +-
src/MC/fix_bond_swap.cpp | 2 +-
src/MC/fix_gcmc.cpp | 34 +-
src/MEAM/pair_meam.cpp | 2 -
src/MISC/compute_ti.cpp | 2 +-
src/MISC/fix_deposit.cpp | 150 +-
src/MISC/fix_deposit.h | 5 +-
src/MISC/fix_efield.cpp | 37 +-
src/MISC/fix_efield.h | 2 +-
src/MISC/fix_evaporate.cpp | 6 +-
src/MISC/fix_oneway.cpp | 3 +-
src/MOLECULE/atom_vec_angle.cpp | 6 +-
src/MOLECULE/atom_vec_bond.cpp | 6 +-
src/MOLECULE/atom_vec_full.cpp | 6 +-
src/MOLECULE/atom_vec_molecular.cpp | 6 +-
src/MOLECULE/atom_vec_template.cpp | 8 +-
src/MOLECULE/pair_lj_cut_tip4p_cut.cpp | 12 +
src/MOLECULE/pair_lj_cut_tip4p_cut.h | 1 +
src/MOLECULE/pair_tip4p_cut.cpp | 1 -
src/Makefile | 2 +-
src/Makefile.lib | 4 +-
src/PERI/atom_vec_peri.cpp | 6 +-
src/PERI/pair_peri_eps.cpp | 13 +-
src/PERI/pair_peri_ves.cpp | 2 +-
src/Purge.list | 6 +
src/REPLICA/fix_event.cpp | 7 +-
src/REPLICA/prd.cpp | 14 +-
src/RIGID/fix_rigid.cpp | 6 +-
src/RIGID/fix_rigid_nh_small.cpp | 1532 ++++
src/RIGID/fix_rigid_nh_small.h | 195 +
src/RIGID/fix_rigid_nph_small.cpp | 92 +
.../fix_rigid_nph_small.h} | 43 +-
src/RIGID/fix_rigid_npt_small.cpp | 104 +
.../fix_rigid_npt_small.h} | 53 +-
src/RIGID/fix_rigid_nve_small.cpp | 28 +
.../fix_rigid_nve_small.h} | 33 +-
src/RIGID/fix_rigid_nvt_small.cpp | 50 +
.../fix_rigid_nvt_small.h} | 48 +-
src/RIGID/fix_rigid_small.cpp | 246 +-
src/RIGID/fix_rigid_small.h | 24 +-
src/RIGID/fix_shake.cpp | 46 +-
src/RIGID/fix_shake.h | 7 +-
src/SHOCK/fix_msst.cpp | 1 -
src/SHOCK/fix_wall_piston.cpp | 2 +-
src/USER-AWPMD/atom_vec_wavepacket.cpp | 6 +-
src/USER-COLVARS/README | 6 +-
src/USER-COLVARS/colvarproxy_lammps.cpp | 1 +
src/USER-COLVARS/fix_colvars.cpp | 40 -
src/USER-COLVARS/group_ndx.cpp | 10 +-
src/USER-CUDA/atom_vec_angle_cuda.cpp | 1 -
src/USER-CUDA/atom_vec_atomic_cuda.cpp | 1 -
src/USER-CUDA/atom_vec_charge_cuda.cpp | 1 -
src/USER-CUDA/atom_vec_full_cuda.cpp | 1 -
src/USER-CUDA/comm_cuda.cpp | 2 +-
src/USER-CUDA/comm_cuda.h | 4 +-
src/USER-CUDA/compute_temp_partial_cuda.cpp | 6 +-
src/USER-EFF/atom_vec_electron.cpp | 6 +-
src/USER-EFF/compute_temp_eff.cpp | 7 +-
src/USER-EFF/compute_temp_region_eff.cpp | 11 +
src/USER-EFF/compute_temp_region_eff.h | 1 +
src/USER-EFF/pair_eff_cut.cpp | 4 +-
src/USER-EFF/pair_eff_inline.h | 6 +-
src/USER-FEP/Install.sh | 51 +
src/USER-FEP/README | 13 +
src/USER-FEP/compute_fep.cpp | 690 ++
src/USER-FEP/compute_fep.h | 109 +
src/{fix_adapt.cpp => USER-FEP/fix_adapt_fep.cpp} | 203 +-
src/{fix_adapt.h => USER-FEP/fix_adapt_fep.h} | 14 +-
.../pair_coul_cut_soft.cpp} | 194 +-
src/USER-FEP/pair_coul_cut_soft.h | 80 +
.../pair_coul_long_soft.cpp} | 265 +-
src/USER-FEP/pair_coul_long_soft.h | 80 +
.../pair_lj_charmm_coul_long_soft.cpp} | 657 +-
src/USER-FEP/pair_lj_charmm_coul_long_soft.h | 107 +
.../pair_lj_cut_coul_cut_soft.cpp} | 166 +-
src/USER-FEP/pair_lj_cut_coul_cut_soft.h | 82 +
.../pair_lj_cut_coul_long_soft.cpp} | 402 +-
src/USER-FEP/pair_lj_cut_coul_long_soft.h | 94 +
.../pair_lj_cut_soft.cpp} | 538 +-
src/USER-FEP/pair_lj_cut_soft.h | 87 +
.../pair_lj_cut_tip4p_long_soft.cpp} | 147 +-
.../pair_lj_cut_tip4p_long_soft.h} | 57 +-
.../pair_tip4p_long_soft.cpp} | 260 +-
.../pair_tip4p_long_soft.h} | 60 +-
src/USER-LB/README | 4 +-
src/USER-LB/fix_lb_fluid.cpp | 119 +-
src/USER-MISC/compute_temp_rotate.cpp | 7 +-
src/USER-MISC/fix_smd.cpp | 2 -
src/USER-MISC/improper_fourier.cpp | 3 +-
src/USER-MISC/pair_cdeam.cpp | 31 +-
src/USER-MISC/pair_coul_diel.cpp | 2 +-
src/USER-MISC/pair_edip.cpp | 8 +-
src/USER-MISC/pair_lj_sf.cpp | 1 -
src/USER-OMP/fix_shear_history_omp.cpp | 2 -
src/USER-OMP/msm_cg_omp.cpp | 2 +-
src/USER-OMP/msm_omp.cpp | 9 +-
src/USER-OMP/pair_comb_omp.cpp | 5 +-
src/USER-OMP/pair_coul_cut_soft_omp.cpp | 160 +
.../pair_coul_cut_soft_omp.h} | 50 +-
...ul_long_omp.cpp => pair_coul_long_soft_omp.cpp} | 129 +-
.../pair_coul_long_soft_omp.h} | 50 +-
src/USER-OMP/pair_eam_alloy_omp.cpp | 2 +-
src/USER-OMP/pair_eam_fs_omp.cpp | 2 +-
src/USER-OMP/pair_edip_omp.cpp | 9 +-
src/USER-OMP/pair_gran_hertz_history_omp.cpp | 6 +-
src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp | 21 +-
...p.cpp => pair_lj_charmm_coul_long_soft_omp.cpp} | 103 +-
src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.h | 48 +
...g_omp.cpp => pair_lj_cut_coul_cut_soft_omp.cpp} | 135 +-
src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.h | 48 +
..._omp.cpp => pair_lj_cut_coul_long_soft_omp.cpp} | 137 +-
src/USER-OMP/pair_lj_cut_coul_long_soft_omp.h | 48 +
src/USER-OMP/pair_lj_cut_soft_omp.cpp | 165 +
.../pair_lj_cut_soft_omp.h} | 50 +-
src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp | 484 ++
src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.h | 53 +
src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp | 131 +-
src/USER-OMP/pair_nm_cut_coul_long_omp.cpp | 6 +-
src/USER-OMP/pair_tip4p_long_soft_omp.cpp | 453 +
src/USER-OMP/pair_tip4p_long_soft_omp.h | 53 +
src/USER-OMP/pppm_cg_omp.cpp | 1 +
src/USER-OMP/pppm_disp_tip4p_omp.cpp | 68 +-
src/USER-REAXC/fix_qeq_reax.cpp | 439 +-
src/USER-REAXC/fix_qeq_reax.h | 5 +-
src/USER-REAXC/fix_reaxc_species.cpp | 12 +-
src/USER-REAXC/pair_reax_c.cpp | 71 +-
src/USER-REAXC/pair_reax_c.h | 11 +-
src/USER-REAXC/reaxc_allocate.cpp | 581 +-
src/USER-REAXC/reaxc_allocate.h | 14 +-
src/USER-REAXC/reaxc_basic_comm.cpp | 317 -
src/USER-REAXC/reaxc_basic_comm.h | 52 -
src/USER-REAXC/reaxc_bond_orders.cpp | 645 +-
src/USER-REAXC/reaxc_bonds.cpp | 33 -
src/USER-REAXC/reaxc_control.cpp | 26 +-
src/USER-REAXC/reaxc_defs.h | 2 +-
src/USER-REAXC/reaxc_ffield.cpp | 63 -
src/USER-REAXC/reaxc_forces.cpp | 282 +-
src/USER-REAXC/reaxc_hydrogen_bonds.cpp | 68 +-
src/USER-REAXC/reaxc_init_md.cpp | 654 +-
src/USER-REAXC/reaxc_init_md.h | 6 -
src/USER-REAXC/reaxc_io_tools.cpp | 1145 +--
src/USER-REAXC/reaxc_list.cpp | 36 -
src/USER-REAXC/reaxc_lookup.cpp | 30 +-
src/USER-REAXC/reaxc_multi_body.cpp | 145 +-
src/USER-REAXC/reaxc_nonbonded.cpp | 109 +-
src/USER-REAXC/reaxc_reset_tools.cpp | 45 +-
src/USER-REAXC/reaxc_system_props.cpp | 113 -
src/USER-REAXC/reaxc_tool_box.cpp | 233 +-
src/USER-REAXC/reaxc_tool_box.h | 6 -
src/USER-REAXC/reaxc_torsion_angles.cpp | 161 -
src/USER-REAXC/reaxc_traj.cpp | 302 -
src/USER-REAXC/reaxc_types.h | 176 +-
src/USER-REAXC/reaxc_valence_angles.cpp | 174 +-
src/USER-REAXC/reaxc_vector.cpp | 289 +-
src/USER-REAXC/reaxc_vector.h | 31 -
src/USER-SPH/atom_vec_meso.cpp | 18 +-
src/USER-SPH/pair_sph_rhosum.cpp | 2 +-
src/VORONOI/README | 2 +-
src/VORONOI/compute_voronoi_atom.cpp | 235 +-
src/VORONOI/compute_voronoi_atom.h | 24 +-
src/WINDOWS/LAMMPS.sln | 36 +
src/WINDOWS/LAMMPS.vcproj | 2957 +++++++
src/WINDOWS/LAMMPS.vsmacros | Bin 0 -> 182784 bytes
src/WINDOWS/README.txt | 78 +
src/WINDOWS/STUBS.vcproj | 156 +
src/WINDOWS/extra/dirent.h | 372 +
src/WINDOWS/extra/erf.h | 19 +
src/WINDOWS/extra/erf_namd.c | 345 +
src/WINDOWS/extra/fftw2/FFTW2dll.dll | Bin 0 -> 263168 bytes
src/WINDOWS/extra/fftw2/FFTW2dll.lib | Bin 0 -> 22998 bytes
src/WINDOWS/extra/fftw2/FFTW2st.lib | Bin 0 -> 404572 bytes
src/WINDOWS/extra/fftw2/RFFTW2dll.dll | Bin 0 -> 481792 bytes
src/WINDOWS/extra/fftw2/RFFTW2dll.lib | Bin 0 -> 35830 bytes
src/WINDOWS/extra/fftw2/RFFTW2st.lib | Bin 0 -> 337962 bytes
src/WINDOWS/extra/fftw2/fftw.h | 421 +
src/WINDOWS/extra/inttypes.h | 305 +
src/WINDOWS/extra/sleep.cpp | 10 +
src/WINDOWS/extra/sleep.h | 1 +
src/WINDOWS/extra/stdint.h | 247 +
src/WINDOWS/extra/sys/time.h | 28 +
src/WINDOWS/extra/unistd.h | 1 +
src/WINDOWS/settings/style_angle.h | 9 +
src/WINDOWS/settings/style_atom.h | 12 +
src/WINDOWS/settings/style_bond.h | 9 +
src/WINDOWS/settings/style_command.h | 16 +
src/WINDOWS/settings/style_compute.h | 44 +
src/WINDOWS/settings/style_dihedral.h | 7 +
src/WINDOWS/settings/style_dump.h | 8 +
src/WINDOWS/settings/style_fix.h | 69 +
src/WINDOWS/settings/style_improper.h | 5 +
src/WINDOWS/settings/style_integrate.h | 3 +
src/WINDOWS/settings/style_kspace.h | 5 +
src/WINDOWS/settings/style_minimize.h | 6 +
src/WINDOWS/settings/style_pair.h | 49 +
src/WINDOWS/settings/style_region.h | 9 +
src/XTC/dump_xtc.cpp | 4 +-
src/accelerator_cuda.h | 6 +-
src/accelerator_kokkos.h | 6 +-
src/atom.cpp | 47 +-
src/atom.h | 2 +
src/atom_vec.cpp | 21 +-
src/atom_vec.h | 4 +-
src/atom_vec_atomic.cpp | 6 +-
src/atom_vec_body.cpp | 9 +-
src/atom_vec_charge.cpp | 6 +-
src/atom_vec_ellipsoid.cpp | 9 +-
src/atom_vec_hybrid.cpp | 6 +-
src/atom_vec_line.cpp | 8 +-
src/atom_vec_sphere.cpp | 6 +-
src/atom_vec_tri.cpp | 8 +-
src/balance.cpp | 208 +-
src/balance.h | 12 +-
src/change_box.cpp | 2 +-
src/comm.cpp | 1967 +----
src/comm.h | 182 +-
src/{comm.cpp => comm_brick.cpp} | 572 +-
src/{comm.h => comm_brick.h} | 61 +-
src/comm_tiled.cpp | 801 ++
src/comm_tiled.h | 98 +
src/compute.cpp | 14 +
src/compute.h | 22 +-
src/compute_atom_molecule.cpp | 2 +-
src/compute_cluster_atom.cpp | 32 +-
src/compute_cluster_atom.h | 2 +-
src/compute_gyration.cpp | 2 +-
src/compute_gyration_molecule.cpp | 2 +-
src/compute_reduce_region.cpp | 4 +-
src/compute_temp.cpp | 7 +-
src/compute_temp.h | 1 -
src/compute_temp_com.cpp | 7 +-
src/compute_temp_com.h | 1 -
src/compute_temp_deform.cpp | 5 +-
src/compute_temp_deform.h | 1 -
src/compute_temp_partial.cpp | 7 +-
src/compute_temp_partial.h | 1 -
src/compute_temp_profile.cpp | 9 +-
src/compute_temp_profile.h | 1 -
src/compute_temp_ramp.cpp | 5 +-
src/compute_temp_ramp.h | 2 +-
src/compute_temp_region.cpp | 12 +-
src/compute_temp_region.h | 1 +
src/compute_temp_sphere.cpp | 9 +-
src/compute_temp_sphere.h | 2 +-
src/create_atoms.cpp | 4 +-
src/create_box.cpp | 5 +-
src/delete_atoms.cpp | 237 +-
src/delete_atoms.h | 2 +
src/delete_bonds.cpp | 2 +-
src/displace_atoms.cpp | 2 +-
src/dump.cpp | 14 +-
src/dump.h | 4 +-
src/dump_cfg.cpp | 4 +-
src/dump_cfg.h | 2 +
src/dump_custom.cpp | 1 +
src/fix.cpp | 1 +
src/fix.h | 4 +-
src/fix_adapt.cpp | 136 +-
src/fix_adapt.h | 3 +
src/fix_addforce.cpp | 31 +-
src/fix_ave_atom.cpp | 6 +-
src/fix_ave_histo.cpp | 1 +
src/fix_ave_spatial.cpp | 4 +
src/fix_aveforce.cpp | 35 +-
src/fix_balance.cpp | 68 +-
src/fix_balance.h | 4 +-
src/fix_group.cpp | 2 +
src/fix_heat.cpp | 13 +-
src/fix_move.cpp | 23 +-
src/fix_nh.cpp | 7 +
src/fix_nve.cpp | 1 +
src/fix_setforce.cpp | 37 +-
src/fix_store_state.cpp | 3 +-
src/fix_wall_region.cpp | 2 +
src/force.cpp | 56 +-
src/force.h | 1 +
src/group.cpp | 39 +-
src/image.cpp | 4 +-
src/input.cpp | 28 +-
src/input.h | 3 +-
src/irregular.cpp | 12 +-
src/irregular.h | 4 +-
src/lammps.cpp | 3 +-
src/library.cpp | 6 +-
src/modify.cpp | 38 +-
src/neigh_request.cpp | 3 +
src/neigh_request.h | 5 +-
src/neighbor.cpp | 19 +-
src/pair.h | 2 +
src/pair_lj_cut_coul_cut.cpp | 1 +
src/read_data.cpp | 53 +-
src/read_dump.cpp | 2 +-
src/read_restart.cpp | 6 +-
src/region.cpp | 75 +-
src/region.h | 3 +-
src/rerun.cpp | 2 +
src/set.cpp | 1 +
src/thermo.cpp | 4 +-
src/variable.cpp | 116 +-
src/variable.h | 4 +-
src/velocity.cpp | 18 +-
src/version.h | 2 +-
src/write_data.cpp | 34 +-
src/write_dump.cpp | 3 +
src/write_restart.cpp | 14 +-
tools/README | 1 +
tools/fep/README | 7 +
tools/fep/bar.py | 88 +
tools/fep/fdti.py | 36 +
tools/fep/fep.py | 23 +
tools/fep/nti.py | 30 +
tools/moltemplate/common/amber/README.TXT | 49 +-
tools/moltemplate/common/amber/amberparm2lt.sh | 88 +-
.../common/amber/amberparm_improper_to_lt.py | 34 +-
.../common/amber/amberparm_pair_to_lt.py | 3 +-
tools/moltemplate/common/gaff.lt | 8907 ++++++++++----------
tools/moltemplate/common/oplsaa/README.TXT | 116 +-
tools/moltemplate/common/oplsaa/oplsaa.txt | 5968 -------------
.../common/oplsaa/oplsaa_moltemplate.py | 287 +-
.../membrane+protein/moltemplate_files/system.lt | 4 +-
.../2bead_heteropolymer/moltemplate_files/2bead.lt | 2 +-
.../AMBER_force_field_examples/WARNING.TXT | 60 +-
.../hexadecane/README_setup.sh | 64 +-
.../hexadecane/moltemplate_files/ch2group.lt | 12 +-
.../hexadecane/moltemplate_files/ch3group.lt | 21 +-
.../hexadecane/moltemplate_files/hexadecane.lt | 57 +-
.../README_remove_irrelevant_info.sh | 52 +
.../hexadecane/run.in.npt | 2 +-
.../waterTIP3P+isobutane/README.TXT | 47 +-
.../waterTIP3P+isobutane/README_setup.sh | 107 +-
.../moltemplate_files/isobutane.lt | 41 +-
.../README_remove_irrelevant_info.sh | 69 +
.../waterTIP3P+isobutane/run.in.npt | 7 +-
.../OPLSAA_force_field_examples/WARNING.TXT | 7 +-
.../ethylene+benzene_PACKMOL/README.TXT | 24 +
.../ethylene+benzene_PACKMOL}/README_run.sh | 0
.../README_setup.sh | 14 +-
.../ethylene+benzene_PACKMOL}/README_visualize.txt | 0
.../ethylene+benzene_PACKMOL/images/benzene.jpg | Bin 0 -> 15032 bytes
.../images/ethylene+benzene_box80x80x80_LR.jpg | Bin 0 -> 130048 bytes
.../images/ethylene.jpg | Bin
.../moltemplate_files/benzene.lt | 51 +
.../moltemplate_files/ethylene.lt | 40 +
.../oplsaa_lt_generator}/AUTHOR.TXT | 0
.../oplsaa_lt_generator/README.TXT | 108 +
.../minimal_versions/README.TXT | 16 +
.../minimal_versions/oplsaa_subset_minimal.prm | 37 +
.../minimal_versions/oplsaa_subset_simplified.prm | 49 +
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 392 +
.../oplsaa_lt_generator/oplsaa_subset.prm | 5127 +++++++++++
.../moltemplate_files/system.lt | 21 +
.../packmol_files/README.TXT | 5 +
.../packmol_files/benzene.xyz | 14 +
.../packmol_files/ethylene.xyz | 8 +
.../packmol_files/mix_ethylene+benzene.inp | 31 +
.../ethylene+benzene_PACKMOL/run.in.npt | 57 +
.../run.in.nvt | 0
.../ethylene/README_setup.sh | 2 +-
.../ethylene/moltemplate_files/ethylene.lt | 24 +-
.../oplsaa_lt_generator/README.TXT | 101 +-
.../minimal_versions/README.TXT | 16 +
.../minimal_versions/oplsaa_subset_minimal.prm | 22 +
.../minimal_versions/oplsaa_subset_simplified.prm | 25 +
.../oplsaa_lt_generator/oplsaa.txt | 5968 -------------
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 287 +-
.../oplsaa_lt_generator/oplsaa_subset.prm | 5125 +++++++++++
.../oplsaa_lt_generator/oplsaa_subset.txt | 3450 --------
.../ethylene/moltemplate_files/system.lt | 2 +-
.../convert_LAMMPS_to_LT_examples/cnad-cnt/cnt.lt | 779 --
.../all_atom_examples/hexadecane/WARNING.TXT | 2 +-
.../hexadecane/moltemplate_files/alkanes.lt | 14 +-
.../hexadecane/moltemplate_files/ch2group.lt | 12 +-
.../hexadecane/moltemplate_files/ch3group.lt | 12 +-
.../hexadecane/moltemplate_files/hexadecane.lt | 51 +-
.../all_atom_examples/hexadecane/run.in.npt | 2 +-
.../nanotube+water/moltemplate_files/README.sh | 7 +-
.../nanotube+water/moltemplate_files/graphene.lt | 121 +-
.../moltemplate_files/graphene_walls.lt | 5 +-
.../nanotube+water/moltemplate_files/graphite.lt | 61 +
.../nanotube+water/moltemplate_files/nanotube.lt | 19 +-
.../nanotube+water/moltemplate_files/spce.lt | 10 +-
.../nanotube+water/moltemplate_files/system.lt | 21 +-
tools/moltemplate/src/moltemplate.sh | 4 +-
tools/moltemplate/src/nbody_by_type.py | 4 +-
tools/moltemplate/src/nbody_by_type_lib.py | 13 +-
tools/moltemplate/src/ttree_lex.py | 2 +-
tools/moltemplate/src/ttree_matrix_stack.py | 16 +-
674 files changed, 149816 insertions(+), 35018 deletions(-)
delete mode 100755 debian/tests/colloid
create mode 100644 doc/Eqs/compute_fep_bar.jpg
create mode 100644 doc/Eqs/compute_fep_bar.tex
create mode 100644 doc/Eqs/compute_fep_fdti.jpg
create mode 100644 doc/Eqs/compute_fep_fdti.tex
create mode 100644 doc/Eqs/compute_fep_fep.jpg
create mode 100644 doc/Eqs/compute_fep_fep.tex
create mode 100644 doc/Eqs/compute_fep_lambda.jpg
create mode 100644 doc/Eqs/compute_fep_lambda.tex
create mode 100644 doc/Eqs/compute_fep_ti.jpg
create mode 100644 doc/Eqs/compute_fep_ti.tex
create mode 100644 doc/Eqs/compute_fep_u.jpg
create mode 100644 doc/Eqs/compute_fep_u.tex
create mode 100644 doc/Eqs/compute_fep_vol.jpg
create mode 100644 doc/Eqs/compute_fep_vol.tex
create mode 100644 doc/Eqs/pair_coul_soft.jpg
create mode 100644 doc/Eqs/pair_coul_soft.tex
create mode 100644 doc/Eqs/pair_lj_soft.jpg
create mode 100644 doc/Eqs/pair_lj_soft.tex
create mode 100644 doc/JPG/coul_soft.jpg
create mode 100644 doc/JPG/lj_soft.jpg
rename doc/{communicate.html => comm_modify.html} (73%)
rename doc/{communicate.txt => comm_modify.txt} (73%)
create mode 100644 doc/comm_style.html
create mode 100644 doc/comm_style.txt
create mode 100644 doc/compute_fep.html
create mode 100644 doc/compute_fep.txt
copy doc/{fix_adapt.html => fix_adapt_fep.html} (84%)
copy doc/{fix_adapt.txt => fix_adapt_fep.txt} (84%)
create mode 100644 doc/pair_lj_soft.html
create mode 100644 doc/pair_lj_soft.txt
create mode 100644 examples/USER/fep/CC-CO/README
create mode 100644 examples/USER/fep/CC-CO/bar01/bar01.lmp
create mode 100644 examples/USER/fep/CC-CO/bar01/in.bar01.lmp
create mode 100644 examples/USER/fep/CC-CO/bar01/log.lammps
create mode 100644 examples/USER/fep/CC-CO/bar10/bar10.lmp
create mode 100644 examples/USER/fep/CC-CO/bar10/in.bar10.lmp
create mode 100644 examples/USER/fep/CC-CO/bar10/log.lammps
create mode 100644 examples/USER/fep/CC-CO/fdti01/fdti01.lmp
create mode 100644 examples/USER/fep/CC-CO/fdti01/in.fdti01.lmp
create mode 100644 examples/USER/fep/CC-CO/fdti01/log.lammps
create mode 100644 examples/USER/fep/CC-CO/fdti10/fdti10.lmp
create mode 100644 examples/USER/fep/CC-CO/fdti10/in.fdti10.lmp
create mode 100644 examples/USER/fep/CC-CO/fdti10/log.lammps
create mode 100644 examples/USER/fep/CC-CO/fep01/data.0.lmp
create mode 100644 examples/USER/fep/CC-CO/fep01/fep01.lmp
create mode 100644 examples/USER/fep/CC-CO/fep01/in.fep01
create mode 100644 examples/USER/fep/CC-CO/fep01/in.fep01.lmp
create mode 100644 examples/USER/fep/CC-CO/fep01/log.lammps
create mode 100644 examples/USER/fep/CC-CO/fep01/log.reference
create mode 100644 examples/USER/fep/CC-CO/fep01/log.reference-omp
create mode 100644 examples/USER/fep/CC-CO/fep10/fep10.lmp
create mode 100644 examples/USER/fep/CC-CO/fep10/in.fep10.lmp
create mode 100644 examples/USER/fep/CC-CO/fep10/log.lammps
create mode 100644 examples/USER/fep/CC-CO/mols/CC-CO.ff
create mode 100644 examples/USER/fep/CC-CO/mols/CC-CO.zmat
create mode 100644 examples/USER/fep/CC-CO/mols/CO-CC.zmat
create mode 100644 examples/USER/fep/CC-CO/mols/README
create mode 100644 examples/USER/fep/CC-CO/mols/data.0.lmp
create mode 100644 examples/USER/fep/CC-CO/mols/data.1.lmp
create mode 100644 examples/USER/fep/CC-CO/mols/spce.ff
create mode 100644 examples/USER/fep/CC-CO/mols/spce.zmat
create mode 100644 examples/USER/fep/CH4-CF4/README
create mode 100644 examples/USER/fep/CH4-CF4/bar01/bar01.lmp
create mode 100644 examples/USER/fep/CH4-CF4/bar01/in.bar01.lmp
create mode 100644 examples/USER/fep/CH4-CF4/bar01/log.lammps
create mode 100644 examples/USER/fep/CH4-CF4/bar10/bar10.lmp
create mode 100644 examples/USER/fep/CH4-CF4/bar10/in.bar10.lmp
create mode 100644 examples/USER/fep/CH4-CF4/bar10/log.lammps
create mode 100644 examples/USER/fep/CH4-CF4/mols/CF4-CH4.zmat
create mode 100644 examples/USER/fep/CH4-CF4/mols/CH4-CF4.ff
create mode 100644 examples/USER/fep/CH4-CF4/mols/CH4-CF4.zmat
create mode 100644 examples/USER/fep/CH4-CF4/mols/data.0.lmp
create mode 100644 examples/USER/fep/CH4-CF4/mols/data.1.lmp
create mode 100644 examples/USER/fep/CH4-CF4/mols/spce.ff
create mode 100644 examples/USER/fep/CH4-CF4/mols/spce.zmat
create mode 100644 examples/USER/fep/CH4hyd/README
create mode 100644 examples/USER/fep/CH4hyd/fdti01/fdti01.lmp
create mode 100644 examples/USER/fep/CH4hyd/fdti01/in.fdti01.lmp
create mode 100644 examples/USER/fep/CH4hyd/fdti01/log.lammps
create mode 100644 examples/USER/fep/CH4hyd/fdti10/fdti10.lmp
create mode 100644 examples/USER/fep/CH4hyd/fdti10/in.fdti10.lmp
create mode 100644 examples/USER/fep/CH4hyd/fdti10/log.lammps
create mode 100644 examples/USER/fep/CH4hyd/fep01/fep01.lmp
create mode 100644 examples/USER/fep/CH4hyd/fep01/in.fep01.lmp
create mode 100644 examples/USER/fep/CH4hyd/fep01/log.lammps
create mode 100644 examples/USER/fep/CH4hyd/fep10/fep10.lmp
create mode 100644 examples/USER/fep/CH4hyd/fep10/in.fep10.lmp
create mode 100644 examples/USER/fep/CH4hyd/fep10/log.lammps
create mode 100644 examples/USER/fep/CH4hyd/mols/data.lmp
create mode 100644 examples/USER/fep/CH4hyd/mols/methane.zmat
create mode 100644 examples/USER/fep/CH4hyd/mols/oplsaa.ff
create mode 100644 examples/USER/fep/CH4hyd/mols/tip4pew.ff
create mode 100644 examples/USER/fep/CH4hyd/mols/tip4pew.zmat
create mode 100644 examples/USER/fep/README
create mode 100644 examples/nb3b/MOH.nb3b.harmonic
create mode 100644 examples/nb3b/data.nb3b
create mode 100644 examples/nb3b/in.nb3b
create mode 100644 examples/nb3b/log.nb3b.1Feb14.linux.1
create mode 100644 examples/nb3b/log.nb3b.1Feb14.linux.4
rename src/KSPACE/{commgrid.cpp => gridcomm.cpp} (97%)
rename src/KSPACE/{commgrid.h => gridcomm.h} (92%)
create mode 100644 src/MAKE/Makefile.bgq
create mode 100644 src/MAKE/Makefile.bgq.details
create mode 100644 src/MAKE/Makefile.ubuntu
create mode 100644 src/MAKE/Makefile.ubuntu_simple
create mode 100644 src/RIGID/fix_rigid_nh_small.cpp
create mode 100644 src/RIGID/fix_rigid_nh_small.h
create mode 100644 src/RIGID/fix_rigid_nph_small.cpp
copy src/{compute_temp.h => RIGID/fix_rigid_nph_small.h} (53%)
create mode 100644 src/RIGID/fix_rigid_npt_small.cpp
copy src/{compute_temp.h => RIGID/fix_rigid_npt_small.h} (54%)
create mode 100644 src/RIGID/fix_rigid_nve_small.cpp
copy src/{USER-EFF/compute_temp_region_eff.h => RIGID/fix_rigid_nve_small.h} (52%)
create mode 100644 src/RIGID/fix_rigid_nvt_small.cpp
copy src/{compute_temp.h => RIGID/fix_rigid_nvt_small.h} (55%)
create mode 100644 src/USER-FEP/Install.sh
create mode 100644 src/USER-FEP/README
create mode 100644 src/USER-FEP/compute_fep.cpp
create mode 100644 src/USER-FEP/compute_fep.h
copy src/{fix_adapt.cpp => USER-FEP/fix_adapt_fep.cpp} (60%)
copy src/{fix_adapt.h => USER-FEP/fix_adapt_fep.h} (90%)
copy src/{USER-MISC/pair_coul_diel.cpp => USER-FEP/pair_coul_cut_soft.cpp} (61%)
create mode 100644 src/USER-FEP/pair_coul_cut_soft.h
copy src/{USER-MISC/pair_coul_diel.cpp => USER-FEP/pair_coul_long_soft.cpp} (52%)
create mode 100644 src/USER-FEP/pair_coul_long_soft.h
copy src/{KSPACE/pair_lj_cut_coul_long.cpp => USER-FEP/pair_lj_charmm_coul_long_soft.cpp} (54%)
create mode 100644 src/USER-FEP/pair_lj_charmm_coul_long_soft.h
copy src/{pair_lj_cut_coul_cut.cpp => USER-FEP/pair_lj_cut_coul_cut_soft.cpp} (69%)
create mode 100644 src/USER-FEP/pair_lj_cut_coul_cut_soft.h
copy src/{KSPACE/pair_lj_cut_coul_long.cpp => USER-FEP/pair_lj_cut_coul_long_soft.cpp} (69%)
create mode 100644 src/USER-FEP/pair_lj_cut_coul_long_soft.h
copy src/{KSPACE/pair_lj_cut_coul_long.cpp => USER-FEP/pair_lj_cut_soft.cpp} (53%)
create mode 100644 src/USER-FEP/pair_lj_cut_soft.h
copy src/{KSPACE/pair_lj_cut_tip4p_long.cpp => USER-FEP/pair_lj_cut_tip4p_long_soft.cpp} (81%)
copy src/{MOLECULE/pair_lj_cut_tip4p_cut.h => USER-FEP/pair_lj_cut_tip4p_long_soft.h} (64%)
copy src/{MOLECULE/pair_tip4p_cut.cpp => USER-FEP/pair_tip4p_long_soft.cpp} (71%)
copy src/{MOLECULE/pair_lj_cut_tip4p_cut.h => USER-FEP/pair_tip4p_long_soft.h} (61%)
create mode 100644 src/USER-OMP/pair_coul_cut_soft_omp.cpp
copy src/{compute_temp.h => USER-OMP/pair_coul_cut_soft_omp.h} (50%)
copy src/USER-OMP/{pair_nm_cut_coul_long_omp.cpp => pair_coul_long_soft_omp.cpp} (50%)
copy src/{compute_temp.h => USER-OMP/pair_coul_long_soft_omp.h} (50%)
copy src/USER-OMP/{pair_lj_charmm_coul_long_omp.cpp => pair_lj_charmm_coul_long_soft_omp.cpp} (62%)
create mode 100644 src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.h
copy src/USER-OMP/{pair_nm_cut_coul_long_omp.cpp => pair_lj_cut_coul_cut_soft_omp.cpp} (51%)
create mode 100644 src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.h
copy src/USER-OMP/{pair_nm_cut_coul_long_omp.cpp => pair_lj_cut_coul_long_soft_omp.cpp} (55%)
create mode 100644 src/USER-OMP/pair_lj_cut_coul_long_soft_omp.h
create mode 100644 src/USER-OMP/pair_lj_cut_soft_omp.cpp
copy src/{compute_temp.h => USER-OMP/pair_lj_cut_soft_omp.h} (51%)
create mode 100644 src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp
create mode 100644 src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.h
create mode 100644 src/USER-OMP/pair_tip4p_long_soft_omp.cpp
create mode 100644 src/USER-OMP/pair_tip4p_long_soft_omp.h
delete mode 100644 src/USER-REAXC/reaxc_basic_comm.cpp
delete mode 100644 src/USER-REAXC/reaxc_basic_comm.h
create mode 100644 src/WINDOWS/LAMMPS.sln
create mode 100644 src/WINDOWS/LAMMPS.vcproj
create mode 100644 src/WINDOWS/LAMMPS.vsmacros
create mode 100644 src/WINDOWS/README.txt
create mode 100644 src/WINDOWS/STUBS.vcproj
create mode 100644 src/WINDOWS/extra/dirent.h
create mode 100644 src/WINDOWS/extra/erf.h
create mode 100644 src/WINDOWS/extra/erf_namd.c
create mode 100644 src/WINDOWS/extra/fftw2/FFTW2dll.dll
create mode 100644 src/WINDOWS/extra/fftw2/FFTW2dll.lib
create mode 100644 src/WINDOWS/extra/fftw2/FFTW2st.lib
create mode 100644 src/WINDOWS/extra/fftw2/RFFTW2dll.dll
create mode 100644 src/WINDOWS/extra/fftw2/RFFTW2dll.lib
create mode 100644 src/WINDOWS/extra/fftw2/RFFTW2st.lib
create mode 100644 src/WINDOWS/extra/fftw2/fftw.h
create mode 100644 src/WINDOWS/extra/inttypes.h
create mode 100644 src/WINDOWS/extra/sleep.cpp
create mode 100644 src/WINDOWS/extra/sleep.h
create mode 100644 src/WINDOWS/extra/stdint.h
create mode 100644 src/WINDOWS/extra/sys/time.h
create mode 100644 src/WINDOWS/extra/unistd.h
create mode 100644 src/WINDOWS/settings/style_angle.h
create mode 100644 src/WINDOWS/settings/style_atom.h
create mode 100644 src/WINDOWS/settings/style_bond.h
create mode 100644 src/WINDOWS/settings/style_command.h
create mode 100644 src/WINDOWS/settings/style_compute.h
create mode 100644 src/WINDOWS/settings/style_dihedral.h
create mode 100644 src/WINDOWS/settings/style_dump.h
create mode 100644 src/WINDOWS/settings/style_fix.h
create mode 100644 src/WINDOWS/settings/style_improper.h
create mode 100644 src/WINDOWS/settings/style_integrate.h
create mode 100644 src/WINDOWS/settings/style_kspace.h
create mode 100644 src/WINDOWS/settings/style_minimize.h
create mode 100644 src/WINDOWS/settings/style_pair.h
create mode 100644 src/WINDOWS/settings/style_region.h
copy src/{comm.cpp => comm_brick.cpp} (72%)
copy src/{comm.h => comm_brick.h} (68%)
create mode 100644 src/comm_tiled.cpp
create mode 100644 src/comm_tiled.h
create mode 100644 tools/fep/README
create mode 100755 tools/fep/bar.py
create mode 100755 tools/fep/fdti.py
create mode 100755 tools/fep/fep.py
create mode 100755 tools/fep/nti.py
delete mode 100644 tools/moltemplate/common/oplsaa/oplsaa.txt
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/README.TXT
copy tools/moltemplate/examples/all_atom_examples/{AMBER_force_field_examples/hexadecane => OPLSAA_force_field_examples/ethylene+benzene_PACKMOL}/README_run.sh (100%)
copy tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/{ethylene => ethylene+benzene_PACKMOL}/README_setup.sh (78%)
copy tools/moltemplate/examples/{CG_biomolecules/membrane+protein => all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL}/README_visualize.txt (100%)
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/images/benzene.jpg
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/images/ethylene+benzene_box80x80x80_LR.jpg
copy tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/{ethylene => ethylene+benzene_PACKMOL}/images/ethylene.jpg (100%)
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt
copy tools/moltemplate/{common/oplsaa => examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator}/AUTHOR.TXT (100%)
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm
create mode 100755 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/system.lt
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/README.TXT
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/ethylene.xyz
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/mix_ethylene+benzene.inp
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/run.in.npt
copy tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/{ethylene => ethylene+benzene_PACKMOL}/run.in.nvt (100%)
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm
delete mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/oplsaa.txt
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
delete mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.txt
delete mode 100644 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnt.lt
create mode 100644 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphite.lt
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/lammps.git
More information about the debian-science-commits
mailing list